Antimicrobial susceptibility and resistome of Actinobacillus pleuropneumoniae in Taiwan: a next-generation sequencing analysis

Actinobacillus pleuropneumoniae infection causes a high mortality rate in porcine animals. Antimicrobial resistance poses global threats to public health. The current study aimed to determine the antimicrobial susceptibilities and probe the resistome of A. pleuropneumoniae in Taiwan. Herein, 133 isolates were retrospectively collected; upon initial screening, 38 samples were subjected to next-generation sequencing (NGS). Over the period 2017-2022, the lowest frequencies of resistant isolates were found for ceftiofur, cephalexin, cephalothin, and enrofloxacin, while the highest frequencies of resistant isolates were found for oxytetracycline, streptomycin, doxycycline, ampicillin, amoxicillin, kanamycin, and florfenicol. Furthermore, most isolates (71.4%) showed multiple drug resistance. NGS-based resistome analysis revealed aminoglycoside- and tetracycline-related genes at the highest prevalence, followed by genes related to beta-lactam, sulfamethoxazole, florphenicol, and macrolide. A plasmid replicon (repUS47) and insertion sequences (IS10R and ISVAp11) were identified in resistant isolates. Notably, the multiple resistance roles of the insertion sequence IS10R were widely proposed in human medicine; however, this is the first time IS10R has been reported in veterinary medicine. Concordance analysis revealed a high consistency of phenotypic and genotypic susceptibility to florphenicol, tilmicosin, doxycycline, and oxytetracycline. The current study reports the antimicrobial characterization of A. pleuropneumoniae for the first time in Taiwan using NGS.

Prevalence of indoor air pollutants from First Nation homes in North Central British Columbia, Canada

Poor indoor air quality poses significant health risks. This study addresses the gap in knowledge regarding the prevalence of indoor air pollutants in remote and rural First Nation communities in north-central British Columbia, Canada. Dust samples from 75 homes were collected and analysed for house dust mites, pet allergens, mould antigens, and bacterial endotoxins. Indoor air quality parameters, including carbon monoxide, carbon dioxide, particulate matter, temperature, and humidity, were measured. A detailed questionnaire on household characteristics and potential pollutant sources was administered. Homes exhibited exposure to multiple pollutants, with wood stove smoke identified as a primary source. Felis domesticus (cat allergen) and Canis familiaris (dog allergen) were prevalent, with detectable levels in 64% and 60% of homes, respectively. Bacterial endotoxins were present in all households. One-third of homes exceeded recommended thresholds for 3 or more pollutants. This study provides critical insights into the prevalence and magnitude of indoor air pollutants, contributing to a broader initiative to characterise respiratory health in First Nations communities. While many homes in First Nations communities had acceptable air quality, one-third of homes exceeded thresholds for 3 or more pollutants. The results can guide ongoing community efforts to address housing concerns and advocate for increased federal funding.

Biodegradation of chemical contamination by lactic acid bacteria: A biological tool for food safety

Chemical pollutants such as mycotoxins and pesticides exert harmful effects on human health such as inflammation, oxidative stress, and cancer. Several strategies were applied for food decontamination, including physicochemical and biological strategies. The present review comprehensively discussed the recent efforts related to the biodegradation of eight food chemical contaminants, including mycotoxins, acrylamide, biogenic amines, N-nitrosamines, polycyclic aromatic hydrocarbons, bisphenol A, pesticides, and heavy metals by lactic acid bacteria (LAB). Biological detoxification by LAB such as Lactobacillus is a promising approach to remove the risks related to the presence of chemical and environmental pollutants in foodstuffs. It is a safe, efficient, environmentally friendly, and low-cost strategy to remove hazardous compounds. LAB can directly decrease these chemical pollutants by degradation or adsorption. Also, it can indirectly reduce the content of these pollutants by reducing their precursors. Hence, LAB can contribute to reducing chemical pollutants in contaminated foods and enhance food safety.

TolC facilitates the intracellular survival and immunomodulation of Salmonella Typhi in human host cells

Salmonella enterica serovar Typhi (S. Typhi) causes typhoid fever, a systemic infection that affects millions of people worldwide. S. Typhi can invade and survive within host cells, such as intestinal epithelial cells and macrophages, by modulating their immune responses. However, the immunomodulatory capability of S. Typhi in relation to TolC-facilitated efflux pump function remains unclear. The role of TolC, an outer membrane protein that facilitates efflux pump function, in the invasion and immunomodulation of S. Typhi, was studied in human intestinal epithelial cells and macrophages. The tolC deletion mutant of S. Typhi was compared with the wild-type and its complemented strain in terms of their ability to invade epithelial cells, survive and induce cytotoxicity in macrophages, and elicit proinflammatory cytokine production in macrophages. The tolC mutant, which has a defective outer membrane, was impaired in invading epithelial cells compared to the wild-type strain, but the intracellular presence of the tolC mutant exhibited greater cytotoxicity and induced higher levels of proinflammatory cytokines (IL-1β and IL-8) in macrophages compared to the wild-type strain. These effects were reversed by complementing the tolC mutant with a functional tolC gene. Our results suggest that TolC plays a role in S. Typhi to efficiently invade epithelial cells and suppress host immune responses during infection. TolC may be a potential target for the development of novel therapeutics against typhoid fever.

A previously unidentified sugar transporter for engineering of high-yield Streptomyces

Sugar transporters have significant contributions to regulate metabolic flux towards products and they are general potential targets for engineering of high-yield microbial cell factories. Streptomyces, well-known producers of natural product pharmaceuticals, contain an abundance of sugar transporters, while few of them are well characterized and applied. Here, we report a previously unidentified ATP-binding cassette (ABC) sugar transporter TP6568 found within a Streptomyces avermitilis transposon library, along with its key regulator GM006564. Subsequent in silico molecular docking and genetic experiments demonstrated that TP6568 possessed a broad substrate specificity. It could not only promote uptake of diverse monosaccharides and disaccharides, but also enhance the utilization of industrial carbon sources such as starch, sucrose, and dextrin. Constitutive overexpression of TP6568 resulted in decrease of residual total sugar by 36.16%, 39.04%, 38.40%, and 30.21% in engineered S. avermitilis S0, Streptomyces caniferus NEAU6, Streptomyces bingchenggensis BC-101-4, and Streptomyces roseosporus NRRL 11379 than their individual parent strain, respectively. Production of avermectin B1a, guvermectin, and milbemycin A3/A4 increased by 75.61%, 56.89%, and 41.13%, respectively. We then overexpressed TP6568 in combination with the regulator GM006564 in a high-yield strain S. avermitilis S45, and further fine-tuning of their overexpression levels boosted production of avermectin B1a by 50.97% to 7.02 g/L in the engineering strain. Our work demonstrates that TP6568 as a promising sugar transporter may have broad applications in construction of high-yield Streptomyces microbial cell factories for desirable natural product pharmaceuticals. KEY POINTS: • TP6568 from Streptomyces avermitilis was identified as a sugar transporter • TP6568 enhanced utilization of diverse industrially used sugars in Streptomyces • TP6568 is a useful transporter to construct high-yield Streptomyces cell factories.

Enzymatic synthesis of Hydroxytyrosol from Oleuropein for valorization of an agricultural waste

Oleuropein (OP) is an appreciated compound present not only in fruits but also in leaves of olive trees, which can be transformed into hydroxytyrosol (HT), a substance with high antioxidant activity. In this work, the transformation of an agricultural residue containing OP (olive leaves or wastewater from mills) to the high added value compound HT is accomplished through different enzymatic strategies. Different enzymes were used, immobilized on various supports by diverse binding forces: beta-glucosidase encapsulated in siliceous material, esterases and lipases immobilized on hydrophobic supports (octyl-functionalized amorphous silica and periodic mesoporous organosilica), and esterase immobilized on amine-functionalized ordered mesoporous silica. All these biocatalysts were tested for oleuropein hydrolysis through two different reaction approaches: a) split of glucosidic bond catalyzed by beta-glucosidase (β-glu), followed by hydrolysis of the aglycon and further ester hydrolysis. 5 mg·mL-1 of β-glu fully hydrolyzed 5 mM OP at pH 7 and 50°C in 7 days, and further enzymatic hydrolysis of the aglycon yielded near to 0.5 mM HT in the best conditions tested. b) via direct hydrolysis of the ester bond to produce hydroxytyrosol in a one-step reaction using esterases or lipases. The latter reaction pathway catalyzed by lipase from Penicillium camemberti immobilized on octyl-silica (4 mg·mL-1) at 35°C and pH 6 directly produced 6.8 mM HT (1 mg·mL-1), transforming in 12 days near to 30% of the initial 25 mM OP from a commercial olive leaves extract.

Sucrose contributed to the biofilm formation of Tetragenococcus halophilus and changed the biofilm structure

Based on the previous research results that the addition of sucrose in the medium improved the biofilm formation of Tetragenococcus halophilus, the influence of sucrose on biofilm formation was explored. Moreover, the influence of exogenous expression of related genes sacA and galE from T. halophilus on the biofilm formation of L. lactis NZ9000 was investigated. The results showed that the addition of sucrose in the medium improved the biofilm formation, the resistance of biofilm cells to freeze-drying stress, and the contents of exopolysaccharides (EPS) and eDNA in the T. halophilus biofilms. Meanwhile, the addition of sucrose in the medium changed the monosaccharide composition of EPS and increased the proportion of glucose and galactose in the monosaccharide composition. Under 2.5% (m/v) salt stress condition, the expression of gene sacA promoted the biofilm formation and the EPS production of L. lactis NZ9000 with the sucrose addition in the medium and changed the EPS monosaccharide composition. The expression of gene galE up-regulated the proportion of rhamnose, galactose, and arabinose in the monosaccharide composition of EPS, and down-regulated the proportion of glucose and mannose. This study will provide a theoretical basis for regulating the biofilm formation of T. halophilus, and provide a reference for the subsequent research on lactic acid bacteria biofilms.

Influence of flor yeast starters on volatile and nitrogen compounds during a controlled biological aging

Fino Sherry wine undergoes biological aging carried out by a velum of flor yeast within a traditional dynamic system known as "criaderas and solera". The complex microbiota of biofilm-forming Saccharomyces cerevisiae strains play a crucial role in shaping the distinctive organoleptic profile of these types of wines. For this reason, the aim of this study is to analyze the changes produced by different flor yeast strains in the volatilome and the aminogram of different wines from the criaderas and solera system during biological aging in the laboratory, simulating a flor yeast velum condition at different stages of the system. Results suggest that each strain metabolizes wine differently, finding that depending on the wine, some strains are better suited for the process than others. In addition, it is found that the content of biogenic amines in Fino Sherry wines, previously attributed to malolactic bacteria, varies according to the yeast strain metabolizing the wine, suggesting that flor yeast could be used to modify biogenic amines content during biological aging. Results indicate that the use of selected flor yeast starters in biological aging may be of interest to modulate some parameters during Fino Sherry wine aging.

Pathogenicity and virulence of Yersinia

The genus Yersinia includes human, animal, insect, and plant pathogens as well as many symbionts and harmless bacteria. Within this genus are Yersinia enterocolitica and the Yersinia pseudotuberculosis complex, with four human pathogenic species that are highly related at the genomic level including the causative agent of plague, Yersinia pestis. Extensive laboratory, field work, and clinical research have been conducted to understand the underlying pathogenesis and zoonotic transmission of these pathogens. There are presently more than 500 whole genome sequences from which an evolutionary footprint can be developed that details shared and unique virulence properties. Whereas the virulence of Y. pestis now seems in apparent homoeostasis within its flea transmission cycle, substantial evolutionary changes that affect transmission and disease severity continue to ndergo apparent selective pressure within the other Yersiniae that cause intestinal diseases. In this review, we will summarize the present understanding of the virulence and pathogenesis of Yersinia, highlighting shared mechanisms of virulence and the differences that determine the infection niche and disease severity.

Pathogenicity and virulence of Acinetobacter baumannii: Factors contributing to the fitness in healthcare settings and the infected host

Acinetobacter baumannii is a common cause of healthcare-associated infections and hospital outbreaks, particularly in intensive care units. Much of the success of A. baumannii relies on its genomic plasticity, which allows rapid adaptation to adversity and stress. The capacity to acquire novel antibiotic resistance determinants and the tolerance to stresses encountered in the hospital environment promote A. baumannii spread among patients and long-term contamination of the healthcare setting. This review explores virulence factors and physiological traits contributing to A. baumannii infection and adaptation to the hospital environment. Several cell-associated and secreted virulence factors involved in A. baumannii biofilm formation, cell adhesion, invasion, and persistence in the host, as well as resistance to xeric stress imposed by the healthcare settings, are illustrated to give reasons for the success of A. baumannii as a hospital pathogen.

Analysis of substrate specificity of cytochrome P450 monooxygenases involved in trichothecene toxin biosynthesis

Trichothecenes are a structurally diverse family of toxic secondary metabolites produced by certain species of multiple fungal genera. All trichothecene analogs share a core 12,13-epoxytrichothec-9-ene (EPT) structure but differ in presence, absence and types of substituents attached to various positions of EPT. Formation of some of the structural diversity begins early in the biosynthetic pathway such that some producing species have few trichothecene biosynthetic intermediates in common. Cytochrome P450 monooxygenases (P450s) play critical roles in formation of trichothecene structural diversity. Within some species, relaxed substrate specificities of P450s allow individual orthologs of the enzymes to modify multiple trichothecene biosynthetic intermediates. It is not clear, however, whether the relaxed specificity extends to biosynthetic intermediates that are not produced by the species in which the orthologs originate. To address this knowledge gap, we used a mutant complementation-heterologous expression analysis to assess whether orthologs of three trichothecene biosynthetic P450s (TRI11, TRI13 and TRI22) from Fusarium sporotrichioides, Trichoderma arundinaceum, and Paramyrothecium roridum can modify trichothecene biosynthetic intermediates that they do not encounter in the organism in which they originated. The results indicate that TRI13 and TRI22 could not modify the intermediates that they do not normally encounter, whereas TRI11 could modify an intermediate that it does not normally encounter. These findings indicate that substrate promiscuity varies among trichothecene biosynthetic P450s. One structural feature that likely impacts the ability of the P450s to use biosynthetic intermediates as substrates is the presence and absence of an oxygen atom attached to carbon atom 3 of EPT.

Endolysin EN572-5 as an alternative to treat urinary tract infection caused by Streptococcus agalactiae

Streptococcus agalactiae (Group B Streptococcus, GBS) is an opportunistic pathogen causing urinary tract infection (UTI). Endolysin EN572-5 was identified in prophage KMB-572-E of the human isolate Streptococcus agalactiae KMB-572. The entire EN572-5 gene was cloned into an expression vector and the corresponding recombinant protein EN572-5 was expressed in Escherichia coli in a soluble form, isolated by affinity chromatography, and characterized. The isolated protein was highly active after 30 min incubation in a temperature range of - 20 °C to 37 °C and in a pH range of 5.5-8.0. The endolysin EN572-5 lytic activity was tested on different Streptococcus spp. and Lactobacillus spp. The enzyme lysed clinical GBS (n = 31/31) and different streptococci (n = 6/8), and also exhibited moderate lytic activity against UPEC (n = 4/4), but no lysis of beneficial vaginal lactobacilli (n = 4) was observed. The ability of EN572-5 to eliminate GBS during UTI was investigated using an in vitro model of UPSA. After the administration of 3 μM EN572-5, a nearly 3-log decrease of urine bacterial burden was detected within 3 h. To date, no studies have been published on the use of endolysins against S. agalactiae during UTI. KEY POINTS: • A lytic protein, EN572-5, from a prophage of a human GBS isolate has been identified. • This protein is easily produced, simple to prepare, and stable after lyophilization. • The bacteriolytic activity of EN572-5 was demonstrated for the first time in human urine.

Enhancing polyethylene degradation: a novel bioprocess approach using Acinetobacter nosocomialis pseudo-resting cells

Despite the discovery of several bacteria capable of interacting with polymers, the activity of the natural bacterial isolates is limited. Furthermore, there is a lack of knowledge regarding the development of bioprocesses for polyethylene (PE) degradation. Here, we report a bioprocess using pseudo-resting cells for efficient degradation of PE. The bacterial strain Acinetobacter nosocomialis was isolated from PE-containing landfills and characterized using low-density PE (LDPE) surface oxidation when incubated with LDPE. We optimized culture conditions to generate catalytic pseudo-resting cells of A. nosocomialis that are capable of degrading LDPE films in a bioreactor. After 28 days of bioreactor operation using pseudo-resting cells of A. nosocomialis, we observed the formation of holes on the PE film (39 holes per 217 cm2, a maximum diameter of 1440 μm). This study highlights the potential of bacteria as biocatalysts for the development of PE degradation processes. KEY POINTS: • New bioprocess has been proposed to degrade polyethylene (PE). • Process with pseudo-resting cells results in the formation of holes in PE film. • We demonstrated PE degradation using A. nosocomialis as a biocatalyst.

Vertical distribution of Candidatus Methylomirabilis and Methanoperedens in agricultural soils

Candidatus Methylomirabilis-related bacteria conduct anaerobic oxidation of methane (AOM) coupling with NO2- reduction, and Candidatus Methanoperedens-related archaea perform AOM coupling with reduction of diverse electron acceptors, including NO3-, Fe (III), Mn (IV) and SO42-. Application of nitrogen fertilization favors the growth of these methanotrophs in agricultural fields. Here, we explored the vertical variations in community structure and abundance of the two groups of methanotrophs in a nitrogen-rich vegetable field via using illumina MiSeq sequencing and quantitative PCR. The retrieved Methylomirabilis-related sequences had 91.12%-97.32% identity to the genomes of known Methylomirabilis species, and Methanoperedens-related sequences showed 85.49%-97.48% identity to the genomes of known Methanoperedens species which are capable of conducting AOM coupling with reduction of NO3- or Fe (III). The Methanoperedens-related archaeal diversity was significantly higher than Methylomirabilis-related bacteria, with totally 74 and 16 operational taxonomic units, respectively. In contrast, no significant difference in abundance between the bacteria (9.19 × 103-3.83 × 105 copies g-1 dry soil) and the archaea (1.55 × 104-3.24 × 105 copies g-1 dry soil) was observed. Furthermore, the abundance of both groups of methanotrophs exhibited a strong vertical variation, which peaked at 30-40 and 20-30 cm layers, respectively. Soil water content and pH were the key factors influencing Methylomirabilis-related bacterial diversity and abundance, respectively. For the Methanoperedens-related archaea, both soil pH and ammonium content contributed significantly to the changes of these archaeal diversity and abundance. Overall, we provide the first insights into the vertical distribution and regulation of Methylomirabilis-related bacteria and Methanoperedens-related archaea in vegetable soils. KEY POINTS: • The archaeal diversity was significantly higher than bacterial. • There was no significant difference in the abundance between bacteria and archaea. • The abundance of bacteria and archaea peaked at 30-40 and 20-30 cm, respectively.

Development of genetic markers in Yarrowia lipolytica

The oleaginous yeast Yarrowia lipolytica represents a potential microbial cell factory for the recombinant production of various valuable products. Currently, the commonly used selection markers for transformation in Y. lipolytica are limited, and successive genetic manipulations are often restricted by the number of available selection markers. In our study, we developed a dominant marker, dsdA, which encodes a D-serine deaminase for genetic manipulation in Y. lipolytica. In Y. lipolytica, this marker confers the ability to use D-serine as a nitrogen source. In addition, the selection conditions of several infrequently used dominant markers including bleoR (zeocin resistance), kanMX (G418 resistance), and guaB (mycophenolic acid resistance) were also analyzed. Our results demonstrated that these selection markers can be used for the genetic manipulation of Y. lipolytica and their selection conditions were different for various strains. Ultimately, the selection markers tested here will be useful to expand the genetic toolbox of Y. lipolytica. KEY POINTS: • The dsdA from Escherichia coli was developed as a dominant marker. • The applicability of several resistance markers in Y. lipolytica was determined. • We introduced the Cre/mutant lox system for marker recycling.

Engineering the Tat-secretion pathway of Bacillus licheniformis for the secretion of cytoplasmic enzyme arginase

The industrial bacterium Bacillus licheniformis has long been used as a microbial factory for the production of enzymes due to its ability to secrete copious amounts of native extracellular proteins and its generally regarded as safe (GRAS) status. However, most attempts to use B. licheniformis to produce heterologous and cytoplasmic enzymes primarily via the general secretory (Sec) pathway have had limited success. The twin-arginine transport (Tat) pathway offers a promising alternative for the extracellular export of Sec-incompatible proteins because it transports full, correctly folded proteins. However, compared to the Sec pathway, the yields of the Tat pathway have historically been too low for commercial use. To improve the export efficiency of the Tat pathway, we identified the optimal Tat-dependent signal peptides and increased the abundance of the Tat translocases, the signal peptidase (SPase), and the intracellular chaperones. These strategic modifications significantly improved the Tat-dependent secretion of the cytoplasmic enzyme arginase into the culture medium using B. licheniformis. The extracellular enzymatic activity of arginase showed a 5.2-fold increase after these modifications. Moreover, compared to the start strain B. licheniformis 0F3, the production of extracellular GFP was improved by 3.8 times using the strategic modified strain B. licheniformis 0F13, and the extracellular enzymatic activity of SOX had a 1.3-fold increase using the strain B. licheniformis 0F14. This Tat-based production chassis has the potential for enhanced production of Sec-incompatible enzymes, therefore expanding the capability of B. licheniformis as an efficient cellular factory for the production of high-value proteins. KEY POINTS: • Systematic genetic modification of Tat-pathway in B. licheniformis. • Significant enhancement of the secretion capacity of Tat pathway for delivery the cytoplasmic enzyme arginase. • A new platform for efficient extracellular production of Sec-incompatible enzymes.

Changes of composition and antibiotic resistance of fecal coliform bacteria in municipal wastewater treatment plant

The dynamics of the composition and antibiotic resistance of the fecal coliform bacteria (FCB) in a typical wastewater treatment plant (WWTP) were investigated concerning the seasonal changes. Results showed that WWTP could remove the FCB concentration by 3∼5 logs within the effluent of 104∼105 CFU/L, but the antibiotic resistant rate of FCB species increased significantly after WWTP. The dominant FCB changed from Escherichia coli in the influent (∼73.0%) to Klebsiella pneumoniae in the effluent (∼53.3%) after WWTP, where the Escherichia coli was removed the most, while Klebsiella pneumoniae was the most persistent. The secondary tank removed the most of FCB (by 3∼4 logs) compared to other processes, but increased all the concerned antibiotic resistant rate. The potential super bugs of FCB community showing resistance to all the target antibiotics were selected in the biological treatment unit of WWTP. The FCB showed the highest multiple antibiotic resistance (92.9%) in total which even increased to 100% in the effluent. Klebsiella has the highest antibiotic resistant rate in FCB, with a multiple antibiotic resistance rate of 98.4%. These indicated that the Klebsiella pneumoniae not just Escherichia coli should be specially emphasized after WWTP concerning the health risk associated with FCB community.

The effect of probiotics and casein supplementation on aerobic capacity parameters of male soccer players

BACKGROUND

In the realm of sports science, nutrition is a well-established pillar for athletes' training, performance, and post-workout recovery. However, the role of gut microbiota, often overlooked, is a novel and intriguing aspect that can significantly impact athletic performance. With this in mind, our study ventures into uncharted territory, investigating the effect of probiotic and casein supplementation on the aerobic capacity of male soccer players.

METHOD

A double-blinded and placebo-controlled study was conducted with 44 male soccer players (Age: 22.81 ± 2.76 yr, Height: 177.90 ± 6.75 cm, Weight: 67.42 ± 8.44 kg). The participants were subjected to the Bruce test in the beginning; then, they were randomly divided into four groups, each consisting of 11 people: probiotics (PRO), casein (CAS), probiotics with casein (PRO+CAS), and placebo (PLA). PRO group was given one probiotic capsule (containing strains of Lactiplantibacillus plantarum BP06, Lacticaseibacillus casei BP07, Lactobacillus acidophilus BA05, Lactobacillus delbrueckii BD08 bulgaricus, Bifidobacterium infantis BI04, Bifidobacterium longum BL03, Bifidobacterium breve BB02 and Streptococcus salivarius thermophilus BT01, with a total dose of 4.5 × 1011 CFU) during dinner, while the CAS group consumed 20 grams of casein powder 45 minutes before bed. The PRO+CAS group was given one probiotic capsule during dinner and 20 grams of casein powder 45 minutes before bed. The participants in the PLA group were given one red capsule (containing 5 grams of starch) during dinner. All participants were instructed to take the supplements only on training days, three times a week for four weeks. The maximal oxygen consumption (VO2max), Ventilatory Threshold (VT), Time-to-exhaustion (TTE), Respiratory Compensation Point (RCP), Isocapnic area Time (Time-IC), Isocapnic area oxygen consumption (VO2-IC), and Hypocapnic Hyperventilation area Time (Time-HHV), after the Bruce test were Measured. All data were analyzed using SPSS Windows software, mixed repeated measure ANOVA, and Bonferroni post hoc test at p < 0.05 level.

RESULTS

The current study's findings illustrated that, after the intervention, TTE (p = 0.01) and RCP (p = 0.01) were significantly improved in PRO+CAS compared to the PLA group. No significant difference was observed between PRO and PLA (p = 0.52), PRO and CAS (p = 0.999), PRO and PRO+CAS (p = 0.9), CAS and PLA (p = 0.65), CAS and PRO+CAS (p = 0.73) in TTE. In addition, no significant difference was observed between PRO and CAS (p = 0.999), PRO and PLA (p = 0.40), PRO and PRO+CAS (p = 0.999), CAS and PLA (p = 0.263), CAS and PRO+CAS (p = 0.999) in RCP. Time-HHV was significantly higher in PRO+CAS (p = 0.000) and CAS (p = 0.047) compared to the PLA group. However, no significant difference was observed in the Time-HHV between PRO and CAS (p = 0.999), PRO and PRO+CAS (p = 0.25), PRO and PLA (p = 0.12), and CAS and PRO+CAS (p = 0.57). Additionally, all the groups had no significant differences in VO2max, VT1, VO2-IC and Time-IC.

CONCLUSION

The findings showed that consuming probiotics and casein could relatively improve the aerobic capacity of male soccer players. Nevertheless, simultaneous consumption of probiotics and casein had a more pronounced effect on aerobic capacity indicators, especially TTE and Time-HHV.

Nucleic acid-binding KH domain proteins influence a spectrum of biological pathways including as part of membrane-localized complexes

K-Homology domain (KH domain) proteins bind single-stranded nucleic acids, influence protein-protein interactions of proteins that harbor them, and are found in all kingdoms of life. In concert with other functional protein domains KH domains contribute to a variety of critical biological activities, often within higher order machineries including membrane-localized protein complexes. Eukaryotic KH domain proteins are linked to developmental processes, morphogenesis, and growth regulation, and their aberrant expression is often associated with cancer. Prokaryotic KH domain proteins are involved in integral cellular activities including cell division and protein translocation. Eukaryotic and prokaryotic KH domains share structural features, but are differentiated based on their structural organizations. In this review, we explore the structure/function relationships of known examples of KH domain proteins, and highlight cases in which they function within or at membrane surfaces. We also summarize examples of KH domain proteins that influence bacterial virulence and pathogenesis. We conclude the article by discussing prospective research avenues that could be pursued to better investigate this largely understudied protein category.

Expression and characterization of monofunctional alcohol dehydrogenase enzymes in Clostridium thermocellum

Clostridium thermocellum is a thermophilic anaerobic bacterium that could be used for cellulosic biofuel production due to its strong native ability to consume cellulose, however its ethanol production ability needs to be improved to enable commercial application. In our previous strain engineering work, we observed a spontaneous mutation in the native adhE gene that reduced ethanol production. Here we attempted to complement this mutation by heterologous expression of 18 different alcohol dehydrogenase (adh) genes. We were able to express all of them successfully in C. thermocellum. Surprisingly, however, none of them increased ethanol production, and several actually decreased it. Our findings contribute to understanding the correlation between C. thermocellum ethanol production and Adh enzyme cofactor preferences. The identification of a set of adh genes that can be successfully expressed in this organism provides a foundation for future investigations into how the properties of Adh enzymes affect ethanol production.

Advances in stress-tolerance elements for microbial cell factories

Microorganisms, particularly extremophiles, have evolved multiple adaptation mechanisms to address diverse stress conditions during survival in unique environments. Their responses to environmental coercion decide not only survival in severe conditions but are also an essential factor determining bioproduction performance. The design of robust cell factories should take the balance of their growing and bioproduction into account. Thus, mining and redesigning stress-tolerance elements to optimize the performance of cell factories under various extreme conditions is necessary. Here, we reviewed several stress-tolerance elements, including acid-tolerant elements, saline-alkali-resistant elements, thermotolerant elements, antioxidant elements, and so on, providing potential materials for the construction of cell factories and the development of synthetic biology. Strategies for mining and redesigning stress-tolerance elements were also discussed. Moreover, several applications of stress-tolerance elements were provided, and perspectives and discussions for potential strategies for screening stress-tolerance elements were made.

Combinatorial metabolic engineering of Escherichia coli for de novo production of structurally defined and homogeneous Amino oligosaccharides

Amino oligosaccharides (AOs) possess various biological activities and are valuable in the pharmaceutical, food industries, and agriculture. However, the industrial manufacturing of AOs has not been realized yet, despite reports on physical, chemical, and biological approaches. In this study, the de novo production of chitin oligosaccharides (CHOS), a type of structurally defined AOs, was achieved in Escherichia coli through combinatorial pathway engineering. The most suitable glycosyltransferase for CHOS production was found to be NodCL from Mesorhizobium Loti. Then, by knocking out the nagB gene to block the flow of N-acetyl-d-glucosamine (NAG) to the glycolytic pathway in E. coli and adjusting the copy number of NodCL-coding gene, the CHOS yield was increased by 6.56 times. Subsequently, by introducing of UDP-N-acetylglucosamine (UDP-GlcNAc) salvage pathway for and optimizing fermentation conditions, the yield of CHOS reached 207.1 and 468.6 mg/L in shake-flask cultivation and a 5-L fed-batch bioreactor, respectively. Meanwhile, the concentration of UDP-GlcNAc was 91.0 mg/L, the highest level reported in E. coli so far. This study demonstrated, for the first time, the production of CHOS with distinct structures in plasmid-free E. coli, laying the groundwork for the biosynthesis of CHOS and providing a starting point for further engineering and commercial production.

A highly efficient method for genomic deletion across diverse lengths in thermophilic Parageobacillus thermoglucosidasius

Parageobacillus thermoglucosidasius is emerging as a highly promising thermophilic organism for metabolic engineering. The utilization of CRISPR-Cas technologies has facilitated programmable genetic manipulation in P. thermoglucosidasius. However, the absence of thermostable NHEJ enzymes limited the capability of the endogenous type I CRISPR-Cas system to generate a variety of extensive genomic deletions. Here, two thermophilic NHEJ enzymes were identified and combined with the endogenous type I CRISPR-Cas system to develop a genetic manipulation tool that can achieve long-range genomic deletion across various lengths. By optimizing this tool-through adjusting the expression level of NHEJ enzymes and leveraging our discovery of a negative correlation between GC content of the guide RNA (gRNA) and deletion efficacy-we streamlined a comprehensive gRNA selection manual for whole-genome editing, achieving a 100 % success rate in randomly selecting gRNAs. Notably, using just one gRNA, we achieved genomic deletions spanning diverse length, exceeding 200 kilobases. This tool will facilitate the genomic manipulation of P. thermoglucosidasius for both fundamental research and applied engineering studies, further unlocking its potential as a thermophilic cell factory.

Co-immunization with DNA vaccines encoding yidR and IL-17 augments host immune response against Klebsiella pneumoniae infection in mouse model

Klebsiella pneumoniae is an important gram-negative bacterium that causes severe respiratory and healthcare-associated infections. Although antibiotic therapy is applied to treat severe infections caused by K. pneumoniae, drug-resistant isolates pose a huge challenge to clinical practices owing to adverse reactions and the mismanagement of antibiotics. Several studies have attempted to develop vaccines against K. pneumoniae, but there are no licensed vaccines available for the control of K. pneumoniae infection. In the current study, we constructed a novel DNA vaccine, pVAX1-YidR, which encodes a highly conserved virulence factor YidR and a recombinant expression plasmid pVAX1-IL-17 encoding Interleukin-17 (IL-17) as a molecular adjuvant. Adaptive immune responses were assessed in immunized mice to compare the immunogenicity of the different vaccine schemes. The results showed that the targeted antigen gene was expressed in HEK293T cells using an immunofluorescence assay. Mice immunized with pVAX1-YidR elicited a high level of antibodies, induced strong cellular immune responses, and protected mice from K. pneumoniae challenge. Notably, co-immunization with pVAX1-YidR and pVAX1-IL-17 significantly augmented host adaptive immune responses and provided better protection against K. pneumoniae infections in vaccinated mice. Our study demonstrates that combined DNA vaccines and molecular adjuvants is a promising strategy to develop efficacious antibacterial vaccines against K. pneumoniae infections.

Unrevealing the potentialities in food formulations of a low-branched dextran from Leuconostoc mesenteroides

The search for novel exopolysaccharides (EPS) with targeted functionalities is currently a topic of great interest. This study aimed to investigate the chemical characteristics and technological properties of a novel EPS (named EPS_O) from Leuconostoc mesenteroides. EPS_O was a high-molecular-weight dextran (>6.68 × 105 g/mol) characterized by high water-holding capacity (785 ± 73%) and high water solubility index (about 99%). EPS_O in water (<30 mg/mL) formed viscous solutions, whereas at concentrations >30 mg/mL, it formed weak gels. Notably, lower concentrations (4-5 mg/mL) exhibited antimicrobial activity against various foodborne pathogens, antibiofilm activity against Listeria monocytogenes, and radical-scavenging activity. These properties are significant for maintaining food quality and promoting health. Based on these findings, EPS_O presents itself as a promising food ingredient that could elevate food quality and confer health benefits to consumers.

The genomic diversity and antimicrobial resistance of Non-typhoidal Salmonella in humans and food animals in Northern India

Introduction

Non-typhoidal Salmonella (NTS) serovars are the leading global cause of gastroenteritis and have established reservoirs in food animals.

Gap statement

Due to a lack of surveillance, there is limited information on the distribution of NTS serovars in India.

Aim

Here, we investigated the epidemiology, sequence types, serovar distribution, phylogenetic relatedness, and antimicrobial resistance patterns of NTS in humans and animals across a large geographic area in Northern India.

Methodology

We collected stool samples from patients with diarrhea who presented to 14 laboratories in Chandigarh and from five states in India (Punjab, Haryana, Uttarakhand, Himachal Pradesh, and Rajasthan). We sequenced the genomes and analyzed 117 NTS organisms isolated from humans and animals. Minimum inhibitory concentrations (MICs) were estimated using a Vitek2 system.

Results

The prevalence of NTS in participants presenting to our study with diarrhea was 1.28 %, affecting all age groups. All NTS caused moderate to severe diarrhea. We found a high diversity of serovars with considerable serovar and sequence types (STs) overlap and phylogenetic closeness between isolates from human infections and food animals. We report serovars such as S. Agona, S. Bareilly, S. Kentucky, S. Saintpaul, and S. Virchow, causing human infections from north India for the first time. Among the different food-producing animals, pigs appeared to be a key source of human infections. Twenty-eight percent (28 %) of the NTS isolates were multi-drug resistant (MDR), and human isolates showed a higher proportion of resistance. A higher level of contamination of meat samples in our study (8.4 %) potentially suggests a close association of NTS serovars with the food chain and high transmission risk in north India.

Conclusions

This study provides information on AMR genes and plasmid replicons associated with different serovars and highlights the role of food animals in AMR dissemination in our region.

The sensor protein AaSho1 regulates infection structures differentiation, osmotic stress tolerance and virulence via MAPK module AaSte11-AaPbs2-AaHog1 in Alternaria alternata

The high-osmolarity-sensitive protein Sho1 functions as a key membrane receptor in phytopathogenic fungi, which can sense and respond to external stimuli or stresses, and synergistically regulate diverse fungal biological processes through cellular signaling pathways. In this study, we investigated the biological functions of AaSho1 in Alternaria alternata, the causal agent of pear black spot. Targeted gene deletion revealed that AaSho1 is essential for infection structure differentiation, response to external stresses and synthesis of secondary metabolites. Compared to the wild-type (WT), the ∆AaSho1 mutant strain showed no significant difference in colony growth, morphology, conidial production and biomass accumulation. However, the mutant strain exhibited significantly reduced levels of melanin production, cellulase (CL) and ploygalacturonase (PG) activities, virulence, resistance to various exogenous stresses. Moreover, the appressorium and infection hyphae formation rates of the ∆AaSho1 mutant strain were significantly inhibited. RNA-Seq results showed that there were four branches including pheromone, cell wall stress, high osmolarity and starvation in the Mitogen-activated Protein Kinase (MAPK) cascade pathway. Furthermore, yeast two-hybrid experiments showed that AaSho1 activates the MAPK pathway via AaSte11-AaPbs2-AaHog1. These results suggest that AaSho1 of A. alternata is essential for fungal development, pathogenesis and osmotic stress response by activating the MAPK cascade pathway via Sho1-Ste11-Pbs2-Hog1.

Porin deficiency or plasmid copy number increase mediated carbapenem-resistant Escherichia coli resistance evolution

This study investigated resistance evolution mechanisms of conjugated plasmids and bacterial hosts under different concentrations of antibiotic pressure. Ancestral strain ECNX52 was constructed by introducing the blaNDM-5-carrying IncX3 plasmid into E. coli C600, and was subjected to laboratory evolution under different concentrations of meropenem pressure. Minimal inhibitory concentrations and conjugation frequency were determined. Fitness of these strains was assessed. Whole genome sequencing and transcriptional changes were performed. Ancestral host or plasmids were recombined with evolved hosts or plasmids to verify plasmid or host factors in resistance evolution. Role of the repA mutation on plasmid copy number was determined. Two out of the four clones (EM2N1 and EM2N3) exhibited four-fold increase in MIC when exposed to a continuous pressure of 2 μg/mL MEM (1/32 MIC), by down regulating expression of outer membrane protein ompF. Besides, all four clones displayed four-fold increase in MIC and higher conjugation frequency when subjected to a continuous pressure of 4 μg/mL MEM (1/16 MIC), attributing to increasing plasmid copy number generated by repA D140Y (GAT→TAT) mutation. Bacterial hosts and conjugative plasmids can undergo resistance evolution under certain concentrations of antimicrobial pressure by reducing the expression of outer membrane proteins or increasing plasmid copy numbers.

Visualizing metagenomic and metatranscriptomic data: A comprehensive review

The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.

Characterization of the diversity of type IV secretion system-encoding plasmids in Acinetobacter

The multi-drug resistant pathogen Acinetobacter baumannii has gained global attention as an important clinical challenge. Owing to its ability to survive on surfaces, its capacity for horizontal gene transfer, and its resistance to front-line antibiotics, A. baumannii has established itself as a successful pathogen. Bacterial conjugation is a central mechanism for pathogen evolution. The epidemic multidrug-resistant A. baumannii ACICU harbours a plasmid encoding a Type IV Secretion System (T4SS) with homology to the E. coli F-plasmid, and plasmids with homologous gene clusters have been identified in several A. baumannii sequence types. However the genetic and host strain diversity, global distribution, and functional ability of this group of plasmids is not fully understood. Using systematic analysis, we show that pACICU2 belongs to a group of almost 120 T4SS-encoding plasmids within four different species of Acinetobacter and one strain of Klebsiella pneumoniae from human and environmental origin, and globally distributed across 20 countries spanning 4 continents. Genetic diversity was observed both outside and within the T4SS-encoding cluster, and 47% of plasmids harboured resistance determinants, with two plasmids harbouring eleven. Conjugation studies with an extensively drug-resistant (XDR) strain showed that the XDR plasmid could be successfully transferred to a more divergent A. baumanii, and transconjugants exhibited the resistance phenotype of the plasmid. Collectively, this demonstrates that these T4SS-encoding plasmids are globally distributed and more widespread among Acinetobacter than previously thought, and that they represent an important potential reservoir for future clinical concern.

Surveillance of SARS-CoV-2 in wastewater by quantitative PCR and digital PCR: a case study in Shijiazhuang city, Hebei province, China

In this study, we reported the first long-term monitoring of SARS-CoV-2 in wastewater in Mainland China from November 2021 to October 2023. The city of Shijiazhuang was employed for this case study. We developed a triple reverse transcription droplet digital PCR (RT-ddPCR) method using triple primer-probes for simultaneous detection of the N1 gene, E gene, and Pepper mild mottle virus (PMMoV) to achieve accurate quantification of SARS-CoV-2 RNA in wastewater. Both the RT-ddPCR method and the commercial multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) method were implemented for the detection of SARS-CoV-2 in wastewater in Shijiazhuang City over a 24-month period. Results showed that SARS-CoV-2 was detected for the first time in the wastewater of Shijiazhuang City on 10 November 2022. The peak of COVID-19 cases occurred in the middle of December 2022, when the concentration of SARS-CoV-2 in the wastewater was highest. The trend of virus concentration increases and decreases forming a "long-tailed" shape in the COVID-19  outbreak and recession cycle. The results indicated that both multiplex RT-ddPCR and RT-qPCR are effective in detecting SARS-CoV-2 in wastewater, but RT-ddPCR is capable of detecting low concentrations of SARS-CoV-2 in wastewater which is more efficient. The SARS-CoV-2 abundance in wastewater is correlated to clinical data, outlining the public health utility of this work.HighlightsFirst long-term monitoring of SARS-CoV-2 in wastewater in Mainland ChinaCOVID-19 outbreak was tracked in Shijiazhuang City from outbreak to containmentWastewater was monitored simultaneously using RT-ddPCR and RT-qPCR methodsTriple primer-probe RT-ddPCR detects N1 and E genes of SARS-CoV-2 and PMMoV.

Pathway crosstalk between the central metabolic and heme biosynthetic pathways in Phanerochaete chrysosporium

A comprehensive analysis to survey heme-binding proteins produced by the white-rot fungus Phanerochaete chrysosporium was achieved using a biotinylated heme-streptavidin beads system. Mitochondrial citrate synthase (PcCS), glyceraldehyde 3-phosphate dehydrogenase (PcGAPDH), and 2-Cys thioredoxin peroxidase (mammalian HBP23 homolog) were identified as putative heme-binding proteins. Among these, PcCS and PcGAPDH were further characterized using heterologously expressed recombinant proteins. Difference spectra of PcCS titrated with hemin exhibited an increase in the Soret absorbance at 414 nm, suggesting that the axial ligand of the heme is a His residue. The activity of PcCS was strongly inhibited by hemin with Ki oxaloacetate of 8.7 μM and Ki acetyl-CoA of 5.8 μM. Since the final step of heme biosynthesis occurred at the mitochondrial inner membrane, the inhibition of PcCS by heme is thought to be a physiological event. The inhibitory mode of the heme was similar to that of CoA analogues, suggesting that heme binds to PcCS at His347 at the AcCoA-CoA binding site, which was supported by the homology model of PcCS. PcGAPDH was also inhibited by heme, with a lower concentration than that for PcCS. This might be caused by the different location of these enzymes. From the integration of these phenomena, it was concluded that metabolic regulations by heme in the central metabolic and heme synthetic pathways occurred in the mitochondria and cytosol. This novel pathway crosstalk between the central metabolic and heme biosynthetic pathways, via a heme molecule, is important in regulating the metabolic balance (heme synthesis, ATP synthesis, flux balance of the tricarboxylic acid (TCA) cycle and cellular redox balance (NADPH production) during fungal aromatic degradation. KEY POINTS: • A comprehensive survey of heme-binding proteins in P. chrysosporium was achieved. • Several heme-binding proteins including CS and GAPDH were identified. • A novel metabolic regulation by heme in the central metabolic pathways was found.

The application of bacteria-derived dehydrogenases and oxidases in the synthesis of gold nanoparticles

In this work the green synthesis of gold nanoparticles (Au-NPs) using the oxidoreductive enzymes Myriococcum thermophilum cellobiose dehydrogenase (Mt CDH), Glomerella cingulata glucose dehydrogenase (Gc GDH), and Aspergillus niger glucose oxidase (An GOX)) as bioreductants was investigated. The influence of reaction conditions on the synthesis of Au-NPs was examined and optimised. The reaction kinetics and the influence of Au ions on the reaction rate were determined. Based on the kinetic study, the mechanism of Au-NP synthesis was proposed. The Au-NPs were characterized by UV-Vis spectroscopy and transmission electron microscopy (TEM). The surface plasmon resonance (SPR) absorption peaks of the Au-NPs synthesised with Mt CDH and Gc GDH were observed at 535 nm, indicating an average size of around 50 nm. According to the image analysis performed on a TEM micrograph, the Au-NPs synthesized with Gc GDH have a spherical shape with an average size of 2.83 and 6.63 nm after 24 and 48 h of the reaction, respectively. KEY POINTS: • The Au NPs were synthesised by the action of enzymes CDH and GDH. • The synthesis of Au-NPs by CDH is related to the oxidation of cellobiose. • The synthesis of Au-NPs by GDH was not driven by the reaction kinetic.

Beauveria bassiana transcriptomics reveal virulence-associated shifts during insect lipid assimilation

Insect cuticular lipids, especially epicuticular hydrocarbons (CHC), have a significant role in insect ecology and interactions with other organisms, including fungi. The CHC composition of a specific insect species may influence the outcome of the interaction with a specific fungal strain. Some insects, such as Piezodorus guildinii, have low susceptibility towards fungal infections seemingly due to their CHC composition. The entomopathogenic fungus Beauveria bassiana can assimilate CHC and incorporate them as building blocks via cytochrome P450 monooxygenases (CYPs). However, little is known about other enzymes that promote the degradation/assimilation of these cuticular components. In this study, we performed a transcriptomic analysis to evaluate the in vitro response of two virulence-contrasting B. bassiana strains when grown on three different P. guildinii CHC sources. We found a different expression profile of virulence-related genes, as well as different GO and KEGG parameters enriched at 4 days post-inoculation, which could help account for the intrinsic virulence and for an alkane-priming virulence enhancement effect. The hypovirulent strain predominantly showed higher expression of cuticle penetration genes, including chitinases, proteases, and CYPs, with GO term categories of "heme binding," "monooxygenase activity," and "peroxisome" pathways enriched. The hypervirulent strain showed higher expression of cell wall remodeling and cell cycle genes, and cuticle adhesion and a distinct set of CYPs, with GO categories of "DNA-binding transcription factor activity" and KEGG pathways corresponding to "meiosis-yeast" and "cell cycle" enriched. These results suggest a delay and alternate routes in pathogenicity-related metabolism in the hypovirulent strain in comparison with the hypervirulent strain. KEY POINTS: •Transcriptomics of two B. bassiana strains grown in P. guildinii cuticular components •Virulence-related genes correlated with virulence enhancement towards P. guildinii •Differentially expressed genes, GOs and KEGGs showed different metabolic timelines associated with virulence.

AMWEst, a new thermostable and detergent-tolerant esterase retrieved from the Albian aquifer

A fosmid library was constructed with the metagenomic DNA from the high-temperature sediment-rich water of the Albian aquifer (Algeria). Functional screening of this library was subsequently done looking for genes encoding lipolytic enzymes. We identified a novel gene named AMWEst (1209 base pairs) encoding a protein of 402 amino acids with a predicted molecular weight of 43.44 kDa and conferring esterase activity. AMWEst was successfully overexpressed in the yeast mesophilic host Saccharomyces cerevisiae, and the expression system used proved to be efficient and produced sufficient activity for its biochemical characterization. Multiple sequence alignment indicated that AMWEst contained a conserved pentapeptide motif (Gly120-His121-Ser122-Gln123-Gly124). The optimum pH and temperature of the recombinant esterase AMWEst were 8 and 80 °C, respectively. Additionally, AMWEst showed higher activity towards short carbon substrates and showed maximum activity for p-nitrophenyl hexanoate (C6). Notably, AMWEst has a remarkable thermostability, and the enzyme retains almost maximum activity at 70 °C after incubation for 1 h. Moreover, enzyme activity was enhanced by high concentrations of SDS and Triton X-100 detergents. KEY POINTS: • A novel thermostable esterase has been retrieved through functional metagenomics • The esterase is detergent-tolerant, which is attractive for some applications • The esterase can be expressed in a yeast mesophilic host to enhance its yield.

Novel yeast-based biosensor for environmental monitoring of tebuconazole

Due to increasing demand for high and stable crop production, human populations are highly dependent on pesticide use for growing and storing food. Environmental monitoring of these agrochemicals is therefore of utmost importance, because of their collateral effects on ecosystem and human health. Even though most current-use analytical methods achieve low detection limits, they require procedures that are too complex and costly for routine monitoring. As such, there has been an increased interest in biosensors as alternative or complementary tools to streamline detection and quantification of environmental contaminants. In this work, we developed a biosensor for environmental monitoring of tebuconazole (TEB), a common agrochemical fungicide. For that purpose, we engineered S. cerevisiae cells with a reporter gene downstream of specific promoters that are expressed after exposure to TEB and characterized the sensitivity and specificity of this model system. After optimization, we found that this easy-to-use biosensor consistently detects TEB at concentrations above 5 μg L-1 and does not respond to realistic environmental concentrations of other tested azoles, suggesting it is specific. We propose the use of this system as a complementary tool in environmental monitoring programs, namely, in high throughput scenarios requiring screening of numerous samples. KEY POINTS: • A yeast-based biosensor was developed for environmental monitoring of tebuconazole. •The biosensor offers a rapid and easy method for tebuconazole detection ≥ 5 μg L-1. •The biosensor is specific to tebuconazole at environmentally relevant concentrations.

Characterization of enteroviruses circulating among farm animals and children in Central African Republic

To characterize enteroviruses (EVs) circulating in farm animals in Central African Republic (CAR), we screened 192 stools of animals under 12 months belonging to family farms located in or near Bangui. To assess whether EV exchanges exist between these animals and humans, we also screened 195 stools of children who lived in contact with farm animals, as well as control stools of 358 children with no contact with farm animals. EVs were typed based on their capsid sequences.In children, all EVs belonged to species A, B and C, with EV-Cs accounting for 60%. Some EV-Cs shared recent common ancestors with lineages of vaccine-derived poliovirus that emerged in the country in 2019-2020. In animals, we identified EV-Gs that belonged to 10 different types, including a previously unknown one that we named EV-G28, while no EV-E or EV-F were observed. The CAR EV-Gs were genetically closely related to specimens sampled in other continents and some of them harboured the torovirus-derived insertion already reported in some EV-Gs. The worldwide circulation of EV-Gs is likely due the massive international trade of live animals. Besides, two human EV-Cs (coxsackievirus A17 and coxsackievirus A24) were detected in pigs, suggesting that these viruses could cross the species barrier. Our work provides original data on the epidemiology and ecology of EVs circulating among herd animals in Africa.

Outer membrane vesicles from genetically engineered Salmonella enterica serovar Typhimurium presenting Helicobacter pylori antigens UreB and CagA induce protection against Helicobacter pylori infection in mice

Helicobacter pylori causes globally prevalent infections that are highly related to chronic gastritis and even development of gastric carcinomas. With the increase of antibiotic resistance, scientists have begun to search for better vaccine design strategies to eradicate H. pylori colonization. However, while current strategies prefer to formulate vaccines with a single H. pylori antigen, their potential has not yet been fully realized. Outer membrane vesicles (OMVs) are a potential platform since they could deliver multiple antigens. In this study, we engineered three crucial H. pylori antigen proteins (UreB, CagA, and VacA) onto the surface of OMVs derived from Salmonella enterica serovar Typhimurium (S. Typhimurium) mutant strains using the hemoglobin protease (Hbp) autotransporter system. In various knockout strategies, we found that OMVs isolated from the ΔrfbP ΔfliC ΔfljB ΔompA mutants could cause distinct increases in immunoglobulin G (IgG) and A (IgA) levels and effectively trigger T helper 1- and 17-biased cellular immune responses, which perform a vital role in protecting against H. pylori. Next, OMVs derived from ΔrfbP ΔfliC ΔfljB ΔompA mutants were used as a vector to deliver different combinations of H. pylori antigens. The antibody and cytokine levels and challenge experiments in mice model indicated that co-delivering UreB and CagA could protect against H. pylori and antigen-specific T cell responses. In summary, OMVs derived from the S. Typhimurium ΔrfbP ΔfliC ΔfljB ΔompA mutant strain as the vector while importing H. pylori UreB and CagA as antigenic proteins using the Hbp autotransporter system would greatly benefit controlling H. pylori infection.

Engineering regioselectivity of glycosyltransferase for efficient polydatin synthesis

Resveratrol is a promising functional ingredient applied in food products. However, low bioavailability and poor water solubility, which can be improved by glycosylation, hinder its application. A uridine diphosphate-dependent glycosyltransferase (UGT) from Bacillus subtilis 168 (named UGTBS) presents potential application for resveratrol glycosylation; nonetheless, imprecise regioselectivity renders the synthesis of resveratrol-3-O-β-D-glucoside (polydatin) difficult. Therefore, molecular evolution was applied to UGTBS. A triple mutant Y14I/I62G/M315W was developed for 3-OH glycosylation of resveratrol and polydatin accounted for 91% of the total product. Kinetic determination and molecular docking indicated that the enhancement of hydrogen bond interaction and altered conformation of the binding pocket increases the enzyme's affinity for the 3-OH group, stabilizing the enzyme-substrate intermediate and promoting polydatin formation. Furthermore, a fed-batch cascade reaction by periodic addition of resveratrol was conducted and nearly 20 mM polydatin was obtained. The mutant Y14I/I62G/M315W can be used for polydatin manufacture.

Analyzing the gut microbiota and microbial-associated metabolites of tomato-based sauces

Red Cooked Sauce (RCS) and Red Raw Sauce (RRS) are a mixture of natural crops that have a promising content of bioactive compounds (BC). The aim was to determine the effect of the indigestible fraction (IF) during the colonic fermentation in RCS and RRS by studying the two-way relationship between gut microbiota composition and microbial metabolites produced from BC fermented in the TNO in vitro dynamic model of the human colon (TIM-2). Total BC in undigested and predigested RRS, 957 and 715 mg/100 g DW, respectively, was significantly higher (p < 0.05) than in the RCS, 571 and 406 mg/100 g DW, respectively. Catenibacterium and Holdemanella increased during RCS fermentation, while 13 genera showed a clear positive correlation with most microbial phenolic metabolites. Our findings suggest that the mechanisms, pathways, and enzymes involved in producing microbial metabolites exhibited uniqueness among bacterial taxa, even within shared genus/family classifications.

Intra-strain colony biofilm heterogeneity in uropathogenic Escherichia coli and the effect of the NlpI lipoprotein

Biofilm growth facilitates the interaction of uropathogenic Escherichia coli (UPEC) with the host environment. The extracellular polymeric substances (EPS) of UPEC biofilms are composed prominently of curli amyloid fiber and cellulose polysaccharide. When the organism is propagated as a colony biofilm on agar media, these macromolecules can generate pronounced macroscopic structures. Moreover, curli/cellulose associate tightly with Congo red, generating a characteristic pink-to-red staining pattern when the media is supplemented with this dye. Among different clinical isolates of UPEC, changes in the abundance of curli/cellulose can lead to diverse colony biofilm phenotypes on a strain-by-strain basis. Nevertheless, for any given isolate, these phenotypes are classically homogenous throughout the colony biofilm. Here, we report that a subset of clinical UPEC isolates display heterogenous 'peppermint' colony biofilms, with distinct pale and red subpopulations. Through isolation of these subpopulations and whole genome sequencing, we demonstrate various emergent mutations associated with the phenomenon, including within the gene encoding the outer membrane lipoprotein nlpI. Deletion of nlpI within independent strain-backgrounds increased biofilm rugosity, while its overexpression induced the peppermint phenotype. Upregulation of EPS-associated proteins and transcripts was likewise observed in the absence of nlpI. Overall, these results demonstrate that EPS elaboration in UPEC is impacted by nlpI. More broadly, this phenomenon of intra-strain colony biofilm heterogeneity may be leveraged as a tool to identify additional members within the broad collection of genes that regulate or otherwise affect biofilm formation.

Intrinsic antimicrobial resistance: Molecular biomaterials to combat microbial biofilms and bacterial persisters

The escalating rise in antimicrobial resistance (AMR) coupled with a declining arsenal of new antibiotics is imposing serious threats to global public health. A pervasive aspect of many acquired AMR infections is that the pathogenic microorganisms exist as biofilms, which are equipped with superior survival strategies. In addition, persistent and recalcitrant infections are seeded with bacterial persister cells at infection sites. Together, conventional antibiotic therapeutics often fail in the complete treatment of infections associated with bacterial persisters and biofilms. Novel therapeutics have been attempted to tackle AMR, biofilms, and persister-associated complex infections. This review focuses on the progress in designing molecular biomaterials and therapeutics to address acquired and intrinsic AMR, and the fundamental microbiology behind biofilms and persisters. Starting with a brief introduction of AMR basics and approaches to tackling acquired AMR, the emphasis is placed on various biomaterial approaches to combating intrinsic AMR, including (1) semi-synthetic antibiotics; (2) macromolecular or polymeric biomaterials mimicking antimicrobial peptides; (3) adjuvant effects in synergy; (4) nano-therapeutics; (5) nitric oxide-releasing antimicrobials; (6) antimicrobial hydrogels; (7) antimicrobial coatings. Particularly, the structure-activity relationship is elucidated in each category of these biomaterials. Finally, illuminating perspectives are provided for the future design of molecular biomaterials to bypass AMR and cure chronic multi-drug resistant (MDR) infections.

Insect hypovirulence-associated mycovirus confers entomopathogenic fungi with enhanced resistance against phytopathogens

Mycoviruses can alter the biological characteristics of host fungi, including change virulence or pathogenicity of phytopathogens and entomopathogenic fungi (EPF). However, most studies on the mycoviruses found in EPF have focused on the effects of the viruses on the virulence of host fungi towards insect pests, with relatively few reports on the effects to the host fungi with regard to plant disease resistance in hosts. The present study investigated the effects of the mycovirus Beauveria bassiana chrysovirus 2 (BbCV2) virus infection on host biological characteristics, evaluated antagonistic activity of BbCV2 against two phytopathogenic fungi (Sclerotinia sclerotiorum and Botrytis cinerea), and transcriptome analysis was used to reveal the interactions between viruses and hosts. Our results showed that BbCV2 virus infection increased B. bassiana's growth rate, spore production, and biomass, it also enhanced the capacity of host fungi and their metabolic products to inhibit phytopathogenic fungi. BbCV2 virus infection reduced the contents of the two pathogens in tomato plants significantly, and transcriptome analysis revealed that the genes related to competition for ecological niches and nutrition, mycoparasitism and secondary metabolites in B. bassiana were significantly up-regulated after viral infection. These findings indicated that the mycovirus infection is an important factor to enhance the ability of B. bassiana against plant disease after endophytic colonization. We suggest that mycovirus infection causes a positive effect on B. bassiana against phytopathogens, which should be considered as a potential strategy to promote the plant disease resistance of EPF.

On-host flea phenology and flea-borne pathogen surveillance among mammalian wildlife of the pineywoods of East Texas

Flea-borne diseases are endemic in Texas, U.S.A., with an increasing incidence of flea-borne typhus and cat scratch disease. Knowledge of flea natural history could provide information to protect public health, yet many knowledge gaps remain outside of plague-endemic regions. Our objective was to characterize seasonal activity patterns of fleas on common mammalian wildlife species and test fleas and wildlife for Rickettsia and Bartonella pathogens. We performed one year of monthly trapping for rodents and medium-sized mammals in a national forest with high recreational use and urban encroachment in East Texas. From 90 mammal captures representing seven species, 101 fleas were collected representing Polygenis spp., Ctenocephalides felis, and Orchopeas species. Virginia opossums (Didelphis virginianus) hosted 99% of the collected fleas (100 fleas) and a single flea was on an eastern woodrat (Neotoma floridana). Flea infestation prevalence of opossums was 79% (23/29). Mean flea abundance was 4.39 fleas, with intensity peaking in spring. One cat flea removed from an opossum was positive for Bartonella henselae. Furthermore, we identified tissue or blood of four raccoons (Procyon lotor) and one golden mouse (Ochrotomys nuttalli) positive for Rickettsia amblyommatis. These findings provide an ecological basis for the maintenance of vectors and pathogens from sylvatic settings.

A comparative study of the efficacy of alginate lyases in the presence of metal ions elevated in the cystic fibrosis lung milieu

Pseudomonas aeruginosa, a common cause of morbidity in cystic fibrosis, chronically infects the patient's lungs by forming an alginate-containing biofilm. Alginate lyases are polysaccharide lyases that lyse alginate and are, therefore, potential biofilm-disruptive agents. However, cystic fibrosis sputum contains high levels of metals such as iron and zinc. The efficacy of alginate lyases under these conditions of elevated metal concentrations has not been categorically determined. Here, we have assessed the enzyme activity of two exolytic and five endolytic alginate lyases in the presence of metal ions (Fe2+, Zn2+, Mn2+, Mg2+, Ca2+, Ni2+, Cu2+) elevated in the cystic fibrosis lung milieu. Several of these alginate lyases exhibited increased activity in the presence of Ca2+, and the polysaccharide lyase family 7 members studied here exhibited decreased activity in the presence of Zn2+. The enzyme activity of the PL7 alginate lyases from Cellulophaga algicola (CaAly/CaFLDAly) and Vibrio sp. (VspAlyVI) was not affected in the presence of a mix of all the above-mentioned metal ions at the elevated concentrations found in the cystic fibrosis lung milieu. Specific alginate lyases might, therefore, retain the ability to degrade the alginate-containing Pseudomonas biofilm in the presence of metal ions elevated in the cystic fibrosis lung milieu.

Characterization of quorum regulatory small RNAs in an emerging pathogen Vibrio fluvialis and their roles toward type VI secretion system VflT6SS2 modulation

The type VI secretion system (T6SS) is essential for Gram-negative bacteria to antagonize a wide variety of prokaryotic and eukaryotic competitors and thus gain survival advantages. Two sets of T6SS have been found in Vibrio fluvialis, namely VflT6SS1 and VflT6SS2, among which VflT6SS2 is functionally expressed. The CqsA/LuxS-HapR quorum sensing (QS) system with CAI-1 and AI-2 as signal molecules can regulate VflT6SS2 by regulators LuxO and HapR, with LuxO repressing while HapR activating VflT6SS2. Quorum regulatory small RNAs (Qrr sRNAs) are Hfq-dependent trans-encoded sRNAs that control Vibrio quorum sensing. In V. fluvialis, Qrr sRNAs have not been characterized and their regulatory function is unknown. In this study, we first identified four Qrr sRNAs in V. fluvialis and demonstrated that these Qrr sRNAs are regulated by LuxO and involved in the modulation of VflT6SS2 function. On the one hand, Qrr sRNAs act on HapR, the activator of both the major and the auxiliary clusters of VflT6SS2, and then indirectly repress VflT6SS2. On the other hand, they directly repress VflT6SS2 by acting on tssB2 and tssD2_a, the first gene of the major cluster and the highly transcriptional one among the two units of the first auxiliary cluster, respectively. Our results give insights into the role of Qrr sRNAs in CAI-1/AI-2 based QS and VflT6SS2 modulation in V. fluvialis and further enhance understandings of the network between QS and T6SS regulation in Vibrio species.

Staphylococcus epidermidis biofilm in inflammatory breast cancer and its treatment strategies

Bacterial biofilms represent a significant challenge in both clinical and industrial settings because of their robust nature and resistance to antimicrobials. Biofilms are formed by microorganisms that produce an exopolysaccharide matrix, protecting function and supporting for nutrients. Among the various bacterial species capable of forming biofilms, Staphylococcus epidermidis, a commensal organism found on human skin and mucous membranes, has emerged as a prominent opportunistic pathogen, when introduced into the body via medical devices, such as catheters, prosthetic joints, and heart valves. The formation of biofilms by S. epidermidis on these surfaces facilitates colonization and provides protection against host immune responses and antibiotic therapies, leading to persistent and difficult-to-treat infections. The possible involvement of biofilms for breast oncogenesis has recently created the curiosity. This paper therefore delves into S. epidermidis biofilm involvement in breast cancer. S. epidermidis biofilms can create a sustained inflammatory environment through their metabolites and can break DNA in breast tissue, promoting cellular proliferation, angiogenesis, and genetic instability. Preventing biofilm formation primarily involves preventing bacterial proliferation using prophylactic measures and sterilization of medical devices and equipment. In cancer treatment, common modalities include chemotherapy, surgery, immunotherapy, alkylating agents, and various anticancer drugs. Understanding the relationship between anticancer drugs and bacterial biofilms is crucial, especially for those undergoing cancer treatment who may be at increased risk of bacterial infections, for improving patient outcomes. By elucidating these interactions, strategies to prevent or disrupt biofilm formation, thereby reducing the incidence of infections associated with medical devices and implants, can be identified.

The effects of AG1® supplementation on the gut microbiome of healthy adults: a randomized, double-blind, placebo-controlled clinical trial

BACKGROUND

This study aimed to examine the effect of a commercially available multi-ingredient powder (AG1Ⓡ) on the gut microbiome and assess the impact of AG1Ⓡ on GI tolerability and other clinical safety markers in healthy men and women.

METHODS

Using a double-blind, randomized, two-arm, placebo-controlled, parallel design, we examined a 4-week daily supplementation regimen of AG1Ⓡ vs. placebo (PL). Fifteen men and 15 women provided stool samples for microbiome analysis, questionnaires for digestive quality of life (DQLQ), and completed visual analog scales (VAS) and Bristol stool charts to assess stool consistency and bowel frequency before and after the 4-week intervention. Participant's blood work (CBC, CMP, and lipid panel) was also assessed before and after the 4-week intervention. Alpha diversity was determined by Shannon and Chao1 index scores and evaluated by a two-way ANOVA, beta diversity in taxonomic abundances and functional pathways was visualized using partial least squares-discriminant analyses and statistically evaluated by PERMANOVA. To identify key biomarkers, specific feature differences in taxonomic relative abundance and normalized functional pathway counts were analyzed by linear discriminant analysis (LDA) effect size (LEfSe). Questionnaires, clinical safety markers, and hemodynamics were evaluated by mixed factorial ANOVAs with repeated measures. This study was registered on clinicaltrials.gov (NCT06181214).

RESULTS

AG1Ⓡ supplementation enriched two probiotic taxa (Lactobacillus acidophilus and Bifidobacterium bifidum) that likely stem from the probiotics species that exist in the product, as well as L. lactis CH_LC01 and Acetatifactor sp900066565 ASM1486575v1 while reducing Clostridium sp000435835. Regarding community function, AG1Ⓡ showed an enrichment of two functional pathways while diminishing none. Alternatively, the PL enriched six, but diminished five functional pathways. Neither treatment negatively impacted the digestive quality of life via DQLQ, bowel frequency via VAS, or stool consistency via VAS and Bristol. However, there may have been a greater improvement in the DQLQ score (+62.5%, p = 0.058, d = 0.73) after four weeks of AG1Ⓡ supplementation compared to a reduction (-50%) in PL. Furthermore, AG1Ⓡ did not significantly alter clinical safety markers following supplementation providing evidence for its safety profile.

CONCLUSIONS

AG1Ⓡ can be consumed safely by healthy adults over four weeks with a potential beneficial impact in their digestive symptom quality of life.

Production of cello-oligosaccharides from corncob residue by degradation-synthesis reactions

The cellulose-rich corncob residue (CCR) is an abundant and renewable agricultural biomass that has been under-exploited. In this study, two strategies were compared for their ability to transform CCR into cello-oligosaccharides (COS). The first strategy employed the use of endo-glucanases. Although selected endo-glucanases from GH9, GH12, GH45, and GH131 could release COS with degrees of polymerization from 2 to 4, the degrading efficiency was low. For the second strategy, first, CCR was efficiently depolymerized to glucose and cellobiose using the cellulase from Trichoderma reesei. Then, using these simple sugars and sucrose as the starting materials, phosphorylases from different microorganisms were combined to generate COS to a level up to 100.3 g/L with different patterns and degrees of polymerization. Using tomato as a model plant, the representative COS obtained from BaSP (a sucrose phosphorylase from Bifidobacterium adolescens), CuCbP (a cellobiose phosphorylase from Cellulomonas uda), and CcCdP (a cellodextrin phosphorylase from Clostridium cellulosi) were shown to be able to promote plant growth. The current study pointed to an approach to make use of CCR for production of the value-added COS. KEY POINTS: • Sequential use of cellulase and phosphorylases effectively generated cello-oligosaccharides from corncob residue. • Cello-oligosaccharides patterns varied in accordance to cellobiose/cellodextrin phosphorylases. • Spraying cello-oligosaccharides promoted tomato growth.

Role of folic acid in regulating gut microbiota and short-chain fatty acids based on an in vitro fermentation model

Folic acid deficiency is common worldwide and is linked to an imbalance in gut microbiota. However, based on model animals used to study the utilization of folic acid by gut microbes, there are challenges of reproducibility and individual differences. In this study, an in vitro fecal slurry culture model of folic acid deficiency was established to investigate the effects of supplementation with 5-methyltetrahydrofolate (MTHF) and non-reduced folic acid (FA) on the modulation of gut microbiota. 16S rRNA sequencing results revealed that both FA (29.7%) and MTHF (27.9%) supplementation significantly reduced the relative abundance of Bacteroidetes compared with control case (34.3%). MTHF supplementation significantly improved the relative abundance of Firmicutes by 4.49%. Notably, compared with the control case, FA and MTHF supplementation promoted an increase in fecal levels of Lactobacillus, Bifidobacterium, and Pediococcus. Short-chain fatty acid (SCFA) analysis showed that folic acid supplementation decreased acetate levels and increased fermentative production of isobutyric acid. The in vitro fecal slurry culture model developed in this study can be utilized as a model of folic acid deficiency in humans to study the gut microbiota and demonstrate that exogenous folic acid affects the composition of the gut microbiota and the level of SCFAs. KEY POINTS: • Establishment of folic acid deficiency in an in vitro culture model. • Folic acid supplementation regulates intestinal microbes and SCFAs. • Connections between microbes and SCFAs after adding folic acid are built.